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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ), 'gf_id' => 'HOM05D001632', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001632' ), 'data_identifier' => 'HOM05D001632', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001632', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p25760' => 'bna', 'A04p00820' => 'bna', 'A04p22420' => 'bna', 'A04p34630' => 'bna', 'A05p01000' => 'bna', 'A05p15950' => 'bna', 'A05p15980' => 'bna', 'A09p54010' => 'bna', 'Aa31LG10G1810' => 'aar', 'Aa31LG10G1840' => 'aar', 'Aa31LG1G28170' => 'aar', 'Aa31LG5G7020' => 'aar', 'Aa31sc60G20' => 'aar', 'Aa31sc60G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4482' => 'aag', 'Actinidia23913' => 'ach', 'Actinidia28082' => 'ach', 'Actinidia34432' => 'ach', 'Ah.13g070850' => 'amhyb', 'AL1G47330' => 'aly', 'AL2G19980' => 'aly', 'AL4G23970' => 'aly', 'AL4G46270' => 'aly', 'AL558U10020' => 'aly', 'AL5G40600' => 'aly', 'AL5G44540' => 'aly', 'Aqoxy1G00804' => 'aox', 'Aqoxy464s002' => 'aox', 'Aqoxy464s003' => 'aox', 'Aqoxy4G02085' => 'aox', 'arahy.Tifrunner.gnm1.ann1.854BZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ARQ7QI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEEP0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NB6CJE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGY3ZU' => 'arhy', 'AT2G29410' => 'ath', 'AT2G46800' => 'ath', 'AT3G58810' => 'ath', 'AT3G61940' => 'ath', 'ATR0757G206' => 'atr', 'Atru.chr3.4022' => 'acertr', 'Atru.chr5.774' => 'acertr', 'Atru.chr8.999' => 'acertr', 'Atru.chr9.1840_Atru.chr9.1842' => 'acertr', 'AUR62004563' => 'cqu', 'BcaB02g10245' => 'bca', 'BcaB02g10246' => 'bca', 'BcaB02g10249' => 'bca', 'BcaB06g28305' => 'bca', 'BcaB06g29472' => 'bca', 'BcaC02g07002' => 'bca', 'BcaC02g08087' => 'bca', 'BcaC02g10265' => 'bca', 'BcaC02g10268' => 'bca', 'BcaC02g12638' => 'bca', 'BcaC03g18506' => 'bca', 'BcaC04g19028' => 'bca', 'BcaC04g19891' => 'bca', 'BcaC07g40690' => 'bca', 'BcaNung03899' => 'bca', 'BcaNung03901' => 'bca', 'BolC4t21767H' => 'bol', 'BolC4t23677H' => 'bol', 'BolC4t24614H' => 'bol', 'BolC4t27375H' => 'bol', 'BolC4t28730H' => 'bol', 'BolC8t51266H' => 'bol', 'BolC9t57867H' => 'bol', 'BolC9t57868H' => 'bol', 'BolC9t59105H' => 'bol', 'BraA03t11790Z' => 'bra', 'BraA04t15800Z' => 'bra', 'BraA04t17790Z' => 'bra', 'BraA04t18921Z' => 'bra', 'BraA05t19100Z' => 'bra', 'BraA09t40815Z' => 'bra', 'C02p08500' => 'bna', 'C04p01140' => 'bna', 'C04p21510' => 'bna', 'C04p30910' => 'bna', 'C04p30960' => 'bna', 'C04p58570' => 'bna', 'C08p36870' => 'bna', 'C09p62670' => 'bna', 'CAN.G169.11' => 'can', 'CAN.G394.80' => 'can', 'CAN.G518.13' => 'can', 'CANSAT21G0333' => 'cansat', 'CANSAT54G1005' => 'cansat', 'CANSAT56G0100' => 'cansat', 'CARHR122690' => 'chi', 'CARHR142140' => 'chi', 'CARHR169240' => 'chi', 'CARHR172300' => 'chi', 'CARHR258230' => 'chi', 'Carub.0004s0943' => 'cru', 'Carub.0004s1047' => 'cru', 'Carub.0004s2951' => 'cru', 'Carub.0005s2559' => 'cru', 'Carub.0005s2870' => 'cru', 'Carub.0006s1212' => 'cru', 'Ca_02027_v3' => 'car', 'Ca_02235_v3' => 'car', 'Ca_20613_v3' => 'car', 'Ca_26487_v3' => 'car', 'Ca_29567_v3' => 'car', 'Cc01_g13470' => 'ccan', 'Cc04_g13860' => 'ccan', 'CDE01G0547' => 'cde', 'CDE02G0309' => 'cde', 'CDE02G2845' => 'cde', 'CDE05G0094' => 'cde', 'CDE05G0651' => 'cde', 'CDE09G0265' => 'cde', 'Cfa011582' => 'cfa', 'Cfa011891' => 'cfa', 'Ciclev10020411m.g' => 'ccl', 'Ciclev10023993m.g' => 'ccl', 'Ciclev10028602m.g' => 'ccl', 'CiPaw.02G045100' => 'cil', 'CiPaw.11G109000' => 'cil', 'CiPaw.12G075300' => 'cil', 'CiPaw.14G064000' => 'cil', 'ClCG03G001210' => 'cla', 'ClCG06G000910' => 'cla', 'COL.COLO4_10839' => 'col', 'COL.COLO4_18596' => 'col', 'COL.COLO4_23053' => 'col', 'COL.COLO4_33277' => 'col', 'Cpa.g.sc37.105' => 'cpa', 'Cpa.g.sc57.86' => 'cpa', 'Cre03.g145087' => 'cre', 'CsaV3_1G034600' => 'csa', 'CsaV3_1G035690' => 'csa', 'CsaV3_6G006770' => 'csa', 'CSS0014621' => 'camsi', 'CSS0028321' => 'camsi', 'CSS0036317' => 'camsi', 'CSS0049997' => 'camsi', 'DCAR_005906' => 'dca', 'DCAR_006569' => 'dca', 'DCAR_007405' => 'dca', 'Dinv17061' => 'din', 'Dinv18773' => 'din', 'Dinv32648' => 'din', 'Dinv43005' => 'din', 'Dinv43092' => 'din', 'Duzib068G0953' => 'dzi', 'Duzib084G0946' => 'dzi', 'Duzib138G0837' => 'dzi', 'Duzib151G1032' => 'dzi', 'Duzib168G1460' => 'dzi', 'Duzib170G0236' => 'dzi', 'ECA236G4859' => 'eca', 'ECA240G3140' => 'eca', 'ECA246G1045' => 'eca', 'EL10Ac1g00182' => 'bvu', 'EL10Ac7g16084' => 'bvu', 'Eucgr.B02299' => 'egr', 'Eucgr.B02300' => 'egr', 'Eucgr.C02043' => 'egr', 'Eucgr.D01642' => 'egr', 'Eucgr.D01644' => 'egr', 'Eucgr.E01082' => 'egr', 'Eucgr.E01084' => 'egr', 'Eucgr.E01087' => 'egr', 'Eucgr.E01088' => 'egr', 'Eucgr.E01089' => 'egr', 'Eucgr.E01090' => 'egr', 'FAN01G0078' => 'fan', 'FAN03G0451' => 'fan', 'FAN04G1452' => 'fan', 'FAN06G1649' => 'fan', 'FAN06G3678' => 'fan', 'FAN08G0351' => 'fan', 'FAN10G1511' => 'fan', 'FAN10G3085' => 'fan', 'FAN11G0574' => 'fan', 'FAN13G1144' => 'fan', 'FAN16G2675' => 'fan', 'FAN18G0335' => 'fan', 'FAN21G2483' => 'fan', 'FAN25G0711' => 'fan', 'FvH4_3g37140' => 'fve', 'FvH4_5g10450' => 'fve', 'FvH4_7g17780' => 'fve', 'Glyma.07G049200' => 'gma', 'Glyma.11G135500' => 'gma', 'Glyma.12G059000' => 'gma', 'Glyma.16G017800' => 'gma', 'Gohir.A02G095400' => 'ghi', 'Gohir.A03G046000' => 'ghi', 'Gohir.A07G100950' => 'ghi', 'Gohir.A08G109000' => 'ghi', 'Gohir.A12G117100' => 'ghi', 'Gohir.D03G088100' => 'ghi', 'Gohir.D03G121200' => 'ghi', 'Gohir.D07G105000' => 'ghi', 'Gohir.D08G121800' => 'ghi', 'Gohir.D12G120700' => 'ghi', 'Gorai.001G112900' => 'gra', 'Gorai.003G073800' => 'gra', 'Gorai.003G128200' => 'gra', 'Gorai.004G128400' => 'gra', 'Gorai.008G131600' => 'gra', 'GSVIVG01019690001' => 'vvi', 'GSVIVG01024865001' => 'vvi', 'GSVIVG01027445001' => 'vvi', 'HanXRQChr05g0135331' => 'han', 'HanXRQChr06g0166691' => 'han', 'HanXRQChr10g0292171' => 'han', 'HanXRQChr13g0415721' => 'han', 'HanXRQChr17g0534091' => 'han', 'Haze_09209' => 'cav', 'Haze_15740' => 'cav', 'Haze_18662' => 'cav', 'Haze_24199' => 'cav', 'Haze_26104' => 'cav', 'Hma1.2p1_0198F.1_g085310' => 'hma', 'Hma1.2p1_0359F.1_g135390' => 'hma', 'Hma1.2p1_0621F.1_g190800' => 'hma', 'HPP92_003678' => 'vpl', 'HPP92_013788' => 'vpl', 'HPP92_013875' => 'vpl', 'HPP92_023744' => 'vpl', 'Hund16754' => 'sun', 'Hund27147' => 'sun', 'Lalb_Chr01g0003451' => 'lal', 'Lalb_Chr03g0026391' => 'lal', 'Lalb_Chr03g0026411' => 'lal', 'Lalb_Chr12g0210671' => 'lal', 'Lalb_Chr17g0343061' => 'lal', 'Lj1g0022688' => 'lja', 'Lj2C151T9' => 'lonja', 'Lj2P1070T25' => 'lonja', 'Lj3g0008292' => 'lja', 'Lj3g0027041' => 'lja', 'Lj9P608T13' => 'lonja', 'Lsat_1_v5_gn_6_82880' => 'lsa', 'Manes.01G239300' => 'mes', 'Manes.02G000600' => 'mes', 'Manes.02G127000' => 'mes', 'Manes.05G016000' => 'mes', 'Mapoly0001s0078' => 'mpo', 'Mapoly0046s0119' => 'mpo', 'Mapoly0059s0099' => 'mpo', 'MBI04_g09605_MAGBIO' => 'mbi', 'MBI05_g02664_MAGBIO' => 'mbi', 'MCO15G189' => 'mco', 'MD01G1089000' => 'mdo', 'MD01G1089100' => 'mdo', 'MD03G1084800' => 'mdo', 'MD06G1123800' => 'mdo', 'MD07G1160600' => 'mdo', 'MD13G1032200' => 'mdo', 'MD14G1140000' => 'mdo', 'MD14G1140800' => 'mdo', 'Medtr2g036390' => 'mtr', 'Medtr4g064893' => 'mtr', 'Medtr8g024240' => 'mtr', 'MELO3C020600.2' => 'cme', 'MELO3C022448.2' => 'cme', 'Migut.D00869' => 'egut', 'Migut.E00719' => 'egut', 'Migut.E01360' => 'egut', 'MSTRG.12222' => 'ama', 'MSTRG.13697' => 'ama', 'MSTRG.2035' => 'ama', 'MSTRG.24878' => 'ama', 'Nitab4.5_0000839g0150' => 'nta', 'Nitab4.5_0001151g0150' => 'nta', 'Nitab4.5_0002988g0010' => 'nta', 'Nitab4.5_0004076g0010' => 'nta', 'Nn1g08890' => 'nnu', 'Nn2g12830' => 'nnu', 'Oeu020478.1' => 'oeu', 'Oeu022025.1' => 'oeu', 'Oeu032143.1' => 'oeu', 'Os05g0128400' => 'osa', 'Peaxi162Scf00347g00120' => 'pax', 'Peaxi162Scf00481g00063' => 'pax', 'Peaxi162Scf00530g00018' => 'pax', 'PGR031G2682' => 'pgr', 'PGR042G0185' => 'pgr', 'PGR102G0718' => 'pgr', 'PGSC0003DMG400030333' => 'stu', 'PGSC0003DMG400030701' => 'stu', 'PGSC0003DMG400030740' => 'stu', 'Phvul.010G119900' => 'pvu', 'Phvul.011G061200' => 'pvu', 'Potri.001G245800' => 'ptr', 'Potri.001G450900' => 'ptr', 'Potri.002G180100' => 'ptr', 'Potri.011G150600' => 'ptr', 'Potri.014G106200' => 'ptr', 'Pp3c2_16170' => 'ppa', 'Pp3c4_30710' => 'ppa', 'PRCOL_00006248' => 'pco', 'Prupe.2G198700' => 'ppe', 'Prupe.5G134300' => 'ppe', 'Prupe.6G068100' => 'ppe', 'Psat1g147440' => 'psa', 'Psat4g164200' => 'psa', 'Psat7g211200' => 'psa', 'PSO063G5676' => 'pso', 'PSO170G1394' => 'pso', 'PSO210G0060' => 'pso', 'PSO210G7556' => 'pso', 'PSO384G4497' => 'pso', 'PSO455G0213' => 'pso', 'PSO676G0015' => 'pso', 'PSO782G4876' => 'pso', 'PSO832G2928' => 'pso', 'QL01p028111' => 'qlo', 'QL02p027170' => 'qlo', 'QL08p047416' => 'qlo', 'QL09p002627' => 'qlo', 'RcHm_v2.0_Chr1g0361171' => 'rch', 'RcHm_v2.0_Chr4g0431771' => 'rch', 'RcHm_v2.0_Chr5g0066861' => 'rch', 'RcHm_v2.0_Chr7g0187761' => 'rch', 'Rhsim01G0180900' => 'rsi', 'Rhsim01G0181100' => 'rsi', 'Rhsim01G0233000' => 'rsi', 'Rhsim02G0254300' => 'rsi', 'Rhsim04G0044600' => 'rsi', 'Sabra09G0027000' => 'sbr', 'Sabra14G0078400' => 'sbr', 'Sabra16G0304600' => 'sbr', 'SalBow6G0891' => 'sbo', 'Sc01g0002170' => 'sci', 'Sc01g0010900' => 'sci', 'Sc12g0001170' => 'sci', 'Sed0003855' => 'sed', 'Sed0010254' => 'sed', 'Sed0025819' => 'sed', 'SEGI_12503' => 'sgi', 'SEGI_37426' => 'sgi', 'SGA_v2.0_scaffold108G30992' => 'sas', 'SGA_v2.0_scaffold31G12744' => 'sas', 'SHI06925' => 'shi', 'SMO270G0121' => 'smo', 'SMO367G0102' => 'smo', 'Solyc06g076440.3' => 'sly', 'Solyc07g007060.3' => 'sly', 'Sopen06g032850' => 'spe', 'Sopen07g003130' => 'spe', 'Sp4g12170' => 'spa', 'Sp4g28830' => 'spa', 'Sp5g01410' => 'spa', 'TAR369G0467' => 'tar', 'TAR375G0297' => 'tar', 'TAR629G0737' => 'tar', 'TAR633G2821' => 'tar', 'THA.LOC104800702' => 'tha', 'THA.LOC104802097' => 'tha', 'THA.LOC104809293' => 'tha', 'THA.LOC104813067' => 'tha', 'THA.LOC104815770' => 'tha', 'THA.LOC104817399' => 'tha', 'Thecc.01G332700' => 'tca', 'Thecc.03G216500' => 'tca', 'Thecc.09G313100' => 'tca', 'Thhalv10001478m.g' => 'esa', 'Thhalv10006388m.g' => 'esa', 'Thhalv10016787m.g' => 'esa', 'TPR.G140' => 'tpr', 'TPR.G19827' => 'tpr', 'TPR.G23568' => 'tpr', 'TPR.G23581' => 'tpr', 'TPR.G32651' => 'tpr', 'TPR.G36424' => 'tpr', 'TPR.G7138' => 'tpr', 'TWI14G0151' => 'twi', 'TWI15G0096' => 'twi', 'TWI31G0964' => 'twi', 'TWI59G0644' => 'twi', 'TWI60G0379' => 'twi', 'TWI75G0431' => 'twi', 'TWI81G0599' => 'twi', 'unitig_744.g24035' => 'ugi', 'unitig_744.g24036' => 'ugi', 'unitig_746.g26717' => 'ugi', 'vmacro04626' => 'vma', 'vmacro11480' => 'vma', 'VMungo0331G0949' => 'vmu', 'VMungo0331G2017' => 'vmu', 'VMungo1127G0631' => 'vmu', 'VMungo1309G1442' => 'vmu', 'Zm00001eb156980' => 'zma', 'Zm00001eb236600' => 'zma', 'Zm00001eb265000' => 'zma', 'Zm00001eb354910' => 'zma', 'Zm00001eb385520' => 'zma', 'Zm00001eb420140' => 'zma' ) $gf_id = 'HOM05D001632' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001632' ) $data_identifier = 'HOM05D001632' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 1, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 4, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 1, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420140' $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